Contacts of the helix formed by residues 293 - 309 (chain D) in PDB entry 1LBI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 293 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D ALA* 3.7 32.1 - - + -
78D GLN* 3.6 41.3 - - + +
79D ILE* 3.5 40.9 - - + -
82D ALA* 3.2 11.7 - - - +
161D PHE* 3.9 11.7 - + - -
274D ASP* 3.8 27.1 - - + -
275D ASP 4.6 2.5 - - - -
276D THR* 4.4 4.5 - - + -
291D GLN* 3.2 42.9 + - + -
292D ASP* 1.3 71.3 + - - +
294D ARG* 1.3 56.4 + - - +
296D LEU* 3.7 7.0 - - - +
297D GLY* 2.9 19.8 + - - -
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Residues in contact with ARG 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ALA* 2.5 43.2 + - + +
85D SER* 2.6 31.1 + - - -
86D ARG* 3.2 23.6 - - - +
89D GLN* 3.8 12.2 + - - -
292D ASP* 3.0 14.5 + - - +
293D PHE* 1.3 75.5 - - - +
295D LEU* 1.3 68.7 + - + +
296D LEU 3.1 0.9 - - - -
297D GLY 3.1 1.0 + - - -
298D GLN* 3.0 28.3 + - - +
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Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D PHE* 5.5 1.8 - - + -
292D ASP* 3.2 28.4 + - + +
294D ARG* 1.3 83.2 - - + +
296D LEU* 1.3 58.4 + - - +
298D GLN* 3.8 15.4 - - - +
299D THR* 2.9 52.0 + - + +
319D LEU* 3.9 24.5 - - + -
320D PRO* 4.9 16.8 - - + +
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Residues in contact with LEU 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ILE* 3.5 48.7 - - + -
148D LEU* 3.9 20.4 - - + +
159D ILE* 3.4 39.9 - - + +
161D PHE* 3.7 21.5 - - + -
292D ASP 3.1 15.1 + - - +
293D PHE 3.7 4.9 - - - +
294D ARG 3.1 0.4 - - - -
295D LEU* 1.3 78.1 - - - +
297D GLY* 1.3 49.7 + - - +
299D THR* 3.7 3.1 - - - -
300D SER* 2.6 35.4 + - - -
319D LEU* 3.6 10.3 - - + +
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Residues in contact with GLY 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ILE* 4.6 2.7 - - - -
82D ALA* 3.8 21.5 - - - +
83D ILE* 4.0 10.5 - - - -
86D ARG* 4.1 0.2 - - - +
293D PHE 2.9 17.3 + - - -
294D ARG 3.1 3.9 + - - -
296D LEU* 1.3 76.2 - - - +
298D GLN* 1.3 59.5 + - - +
300D SER* 3.3 8.1 + - - -
301D VAL* 3.0 29.5 - - - +
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Residues in contact with GLN 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ARG* 3.3 35.0 - - - +
89D GLN* 5.3 0.4 - - - +
294D ARG* 3.0 28.4 + - - +
295D LEU* 3.8 16.0 - - - +
297D GLY* 1.3 76.1 - - - +
299D THR* 1.3 75.7 + - - +
301D VAL 3.5 0.5 + - - -
302D ASP* 2.7 53.0 + - - +
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Residues in contact with THR 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE* 3.9 16.3 - - - +
295D LEU* 2.9 39.1 + - + +
296D LEU* 3.4 9.0 + - - -
298D GLN* 1.3 86.9 - - - +
300D SER* 1.3 55.4 + - - +
302D ASP* 3.7 5.7 - - - +
303D ARG* 2.7 38.3 + - - +
319D LEU* 3.8 17.1 - - + +
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Residues in contact with SER 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ILE* 4.3 6.9 - - - +
123D ILE* 4.7 6.0 - - - +
146D LEU* 3.3 20.2 - - - +
148D LEU* 3.4 37.9 - - - +
159D ILE* 4.1 2.7 - - - -
296D LEU* 2.6 26.4 + - - -
297D GLY* 3.3 10.6 + - - -
299D THR* 1.3 77.3 + - - +
301D VAL* 1.3 58.8 + - - +
304D LEU* 2.9 27.9 + - - +
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Residues in contact with VAL 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 3.7 32.3 - - + -
83D ILE* 3.9 24.2 - - + +
86D ARG* 3.8 9.2 - - + -
87D ALA* 4.5 5.2 - - - +
90D LEU* 3.6 28.7 - - + -
92D ALA* 6.0 1.1 - - + -
123D ILE* 5.1 2.2 - - + -
297D GLY 3.0 21.6 + - - +
298D GLN 3.8 3.6 - - - +
299D THR 3.3 0.4 - - - -
300D SER* 1.3 73.8 + - - +
302D ASP* 1.3 67.0 + - - +
304D LEU* 3.0 7.0 + - - +
305D LEU* 2.9 32.1 + - + +
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Residues in contact with ASP 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ARG* 3.0 39.9 + - - -
90D LEU* 3.6 9.7 - - - +
298D GLN* 2.7 33.8 + - - +
299D THR* 3.8 4.9 + - - +
301D VAL* 1.3 75.0 - - - +
303D ARG* 1.3 64.1 + - - +
305D LEU* 3.1 9.1 + - - +
306D GLN* 3.0 31.5 + - - +
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Residues in contact with ARG 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 3.6 20.3 - - + +
157D ASN* 3.7 11.3 - - - +
158D SER 3.0 24.7 + - - -
159D ILE* 3.6 11.2 - - + +
299D THR 2.7 22.7 + - - +
300D SER 4.0 2.7 - - - +
302D ASP* 1.3 73.9 - - - +
304D LEU* 1.3 56.9 + - - +
306D GLN* 3.4 18.4 + - + +
307D LEU* 3.0 32.1 + - + +
312D ALA 4.9 6.2 + - - +
313D VAL* 4.1 5.6 + - - +
314D LYS* 3.6 9.3 - - - +
315D GLY 3.1 38.2 + - - +
317D GLN* 3.2 44.0 - - - +
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ILE* 4.3 13.0 - - + -
121D GLY* 3.5 29.6 - - - -
122D LEU 3.5 4.9 - - - +
123D ILE* 3.2 32.1 - - + -
144D PRO* 3.4 39.0 - - + +
146D LEU* 4.7 6.7 - - + +
300D SER 2.9 18.7 + - - +
301D VAL* 3.0 5.1 + - - +
303D ARG* 1.3 75.5 - - - +
305D LEU* 1.3 56.7 + - + +
307D LEU* 3.1 9.1 + - + -
308D SER* 2.6 37.1 + - - -
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Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LEU* 4.6 10.3 - - - +
64D ILE* 4.1 24.7 - - + -
90D LEU* 3.2 39.3 - - + -
92D ALA* 5.6 7.6 - - + -
120D SER* 5.8 0.7 - - - +
301D VAL* 2.9 23.4 + - + +
302D ASP* 3.1 6.9 + - - +
304D LEU* 1.3 77.2 - - + +
306D GLN* 1.3 58.5 + - - +
308D SER* 3.2 25.6 + - - +
309D GLN* 3.4 9.7 + - - +
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Residues in contact with GLN 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D ASP* 3.0 22.2 + - - +
303D ARG* 3.4 26.4 + - + +
305D LEU* 1.3 75.2 - - - +
307D LEU* 1.3 62.9 + - - +
308D SER 3.1 1.1 - - - -
309D GLN* 3.1 9.8 + - - +
311D GLN* 3.0 58.0 + - + +
312D ALA 5.8 0.4 - - - +
313D VAL* 4.8 11.9 - - - +
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PRO* 3.8 24.1 - - + +
145D ALA 4.6 4.0 - - - +
146D LEU* 4.0 14.1 - - + -
157D ASN* 3.2 45.1 - - + +
303D ARG* 3.0 25.5 + - + +
304D LEU* 3.5 9.2 - - + +
306D GLN* 1.3 74.2 - - - +
308D SER* 1.3 59.3 + - - +
309D GLN 2.4 18.7 - - - +
310D GLY* 4.6 0.9 - - - -
311D GLN 3.6 15.3 - - - +
312D ALA* 4.8 9.9 - - - +
314D LYS* 5.1 7.6 - - + -
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Residues in contact with SER 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D SER* 5.1 12.7 - - - -
144D PRO* 3.7 18.4 - - - +
304D LEU* 2.6 19.6 + - - -
305D LEU* 3.2 22.6 + - - +
307D LEU* 1.3 72.9 - - - +
309D GLN* 1.3 70.7 + - - +
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Residues in contact with GLN 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D LEU 3.4 9.3 + - - +
306D GLN* 3.1 9.9 + - - +
307D LEU 2.4 24.4 - - - +
308D SER* 1.3 84.8 + - - +
310D GLY* 1.3 54.9 + - - +
311D GLN* 2.9 41.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il